Merge pull request #8 from biothings/tidy_CUI

SemMedDB V43 update

README.md

@@ -1 +1,33 @@
-# SEMMED API parser 08/2021
+# SemMedDB Predication Parser
+
+## Source Data Files
+
+There are four files required by this parser:
+
+1. The _PREDICATION_ CSV file. 
+    - Version: `semmedVER43_R`
+    - Download page: https://lhncbc.nlm.nih.gov/ii/tools/SemRep_SemMedDB_SKR/SemMedDB_download.html
+    - Direct download link: https://data.lhncbc.nlm.nih.gov/umls-restricted/ii/tools/SemRep_SemMedDB_SKR/semmedVER43_2022_R_PREDICATION.csv.gz
+    - Filename: `semmedVER43_2022_R_PREDICATION.csv.gz`
+2. The _Semantic Type Mappings_ file.
+    - Version: `2018AB` (UMLS release version number, as shown in [UMLS Release File Archives](https://www.nlm.nih.gov/research/umls/licensedcontent/umlsarchives04.html))
+    - Download page: https://lhncbc.nlm.nih.gov/ii/tools/MetaMap/documentation/SemanticTypesAndGroups.html
+    - Direct download link: https://lhncbc.nlm.nih.gov/ii/tools/MetaMap/Docs/SemanticTypes_2018AB.txt
+    - Filenname: `SemanticTypes_2018AB.txt`
+3. The _Retired CUI Mapping_ file.
+    - Version: `2022AA` (UMLS release version number, as shown in [UMLS Release File Archives](https://www.nlm.nih.gov/research/umls/licensedcontent/umlsarchives04.html))
+    - Download page: this file is part of the [_2022AA UMLS Metathesaurus Full Subset_](https://www.nlm.nih.gov/research/umls/licensedcontent/umlsarchives04.html); no direct download link is available.
+    - Description: https://www.ncbi.nlm.nih.gov/books/NBK9685/table/ch03.T.retired_cui_mapping_file_mrcui_rr/
+    - Filename: `MRCUI.RRF`
+4. The _Preferred CUI Names & Semtypes_ file.
+    - Github Repo: https://github.com/erikyao/UMLS_CUI_Semtype
+    - How to Generate:
+        - Source data files:
+            - The _Retired CUI Mapping_ file, `MRCUI.RRF` (see above).
+            - The _Concept Names and Sources_ file, `MRCONSO.RRF`.
+                - Version: `2022AA`
+                - Download page: https://www.nlm.nih.gov/research/umls/licensedcontent/umlsarchives04.html
+                - Description: https://www.ncbi.nlm.nih.gov/books/NBK9685/table/ch03.T.concept_names_and_sources_file_mr/
+            - The _Semantic Type Mappings_ file, `SemanticTypes_2018AB.txt` (see above).
+        - Script: [parser.py](https://github.com/erikyao/UMLS_CUI_Semtype/blob/main/parser.py)
+    - Filename: `UMLS_CUI_Semtype.tsv`, as shown [here](https://github.com/erikyao/UMLS_CUI_Semtype/blob/main/parser.py#L188)

manifest.json

@@ -1,14 +1,17 @@
 {
-    "version": "0.1",
-    "requires" : "pyyaml",
+    "version": "0.2",
     "__metadata__" : {
-        "license_url" : "https://skr3.nlm.nih.gov/SemMedDB/",
-        "licence" : "CC BY 4.0",
-        "url" : "https://skr3.nlm.nih.gov/SemMedDB/"
+        "license_url" : "https://lhncbc.nlm.nih.gov/ii/tools/SemRep_SemMedDB_SKR.html",
+        "licence" : "UMLS Metathesaurus License",
+        "url" : "https://lhncbc.nlm.nih.gov/ii/tools/SemRep_SemMedDB_SKR.html"
     },
     "dumper" : {
-        "data_url" : ["https://dl.dropboxusercontent.com/s/im2ru5epalfr9lt/semmed_source.tar.gz",
-                      "https://metamap.nlm.nih.gov/Docs/SemanticTypes_2013AA.txt"],
+        "data_url" : [
+            "https://data.lhncbc.nlm.nih.gov/umls-restricted/ii/tools/SemRep_SemMedDB_SKR/semmedVER43_2022_R_PREDICATION.csv.gz",
+            "https://lhncbc.nlm.nih.gov/ii/tools/MetaMap/Docs/SemanticTypes_2018AB.txt",
+            "http://localhost:8080/dataupload/mysrc/semmeddb/MRCUI.RRF",
+            "http://localhost:8080/dataupload/mysrc/semmeddb/UMLS_CUI_Semtype.tsv"
+        ],
         "uncompress" : true,
         "release" : "version:get_release"
     },